0.016033
0.009257
0.000000
0.000000
0.018514
0.000000
0.000000
0.000000
0.085251
0.000000
0.000000
0.000000
Zhao, M.
Liu, C.
Sawaya, M.R.
Eisenberg, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.000
90.000
120.000
62.370
62.370
11.730
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
Na 1
22.990
SODIUM ION
non-polymer
C16 H34 O8
354.436
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
C
N
7
N
O
N
8
N
O
N
9
N
O
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
O
N
18
N
H
N
19
N
H
N
20
N
N
N
21
S
C
N
22
N
C
N
23
N
O
N
24
N
C
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
N
N
29
N
O
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
NA
N
46
N
O
N
47
N
C
N
48
N
C
N
49
N
O
N
50
N
C
N
51
N
C
N
52
N
O
N
53
N
C
N
54
N
C
N
55
N
O
N
56
N
C
N
57
N
C
N
58
N
O
N
59
N
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
C
N
66
N
C
N
67
N
O
N
68
N
C
N
69
N
C
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
N
N
105
S
C
N
106
N
C
N
107
N
O
N
108
N
C
Y
109
N
C
Y
110
N
C
Y
111
N
C
Y
112
N
C
Y
113
N
C
Y
114
N
C
N
115
N
O
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
S
C
N
129
N
C
N
130
N
O
N
131
N
C
N
132
N
O
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
N
N
142
S
C
N
143
N
C
N
144
N
O
N
145
N
C
Y
146
N
C
Y
147
N
C
Y
148
N
C
Y
149
N
N
Y
150
N
C
Y
151
N
C
Y
152
N
C
Y
153
N
C
Y
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
N
N
169
S
C
N
170
N
C
N
171
N
O
N
172
N
C
Y
173
N
C
Y
174
N
C
Y
175
N
C
Y
176
N
C
Y
177
N
C
Y
178
N
C
N
179
N
O
N
180
N
O
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
doub
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
doub
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
Y
110
N
doub
Y
111
N
sing
Y
112
N
sing
N
113
N
sing
Y
114
N
doub
N
115
N
sing
Y
116
N
doub
N
117
N
sing
Y
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
Y
146
N
doub
Y
147
N
sing
Y
148
N
sing
N
149
N
sing
Y
150
N
doub
Y
151
N
sing
Y
152
N
sing
N
153
N
sing
Y
154
N
sing
Y
155
N
doub
N
156
N
sing
Y
157
N
doub
N
158
N
sing
Y
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
Y
174
N
doub
Y
175
N
sing
Y
176
N
sing
N
177
N
sing
Y
178
N
doub
N
179
N
sing
Y
180
N
doub
N
181
N
sing
Y
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
109
20913
20918
10.1073/pnas.1218792109
23213214
Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates.
2012
10.2210/pdb4e0k/pdb
pdb_00004e0k
100
1
CCD
2010-12-11
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.97911
1.0
137939
0.069
0.970
29973
99.30
24-ID-C
APS
0.97911
SYNCHROTRON
APS BEAMLINE 24-ID-C
845.918
Amyloidogenic peptide segment KDWSFY
4
syn
polymer
354.436
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
2
syn
non-polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
49
nat
water
no
no
KDWSFY
KDWSFY
A,B,C,D
polypeptide(L)
n
n
n
n
n
n
1
1.95
36.81
VAPOR DIFFUSION, HANGING DROP
6.5
0.1M BIS-TRIS PROPANE pH 6.5, 0.2 M SODIUM FLUORIDE, 20% (w/v) PEG 3350, vapor diffusion, hanging drop, temperature 290K
290
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
1
0
2012-12-19
1
1
2013-06-19
1
2
2024-02-28
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-03-04
REL
REL
0.046
599
98.20
0.060
806
99.80
0.058
949
100.00
0.062
1039
100.00
0.067
1224
100.00
0.071
1286
100.00
0.080
1400
100.00
0.088
1437
100.00
0.102
1599
100.00
0.120
1583
100.00
0.140
1769
100.00
0.144
1788
100.00
0.110
1795
98.50
0.122
1981
99.30
0.147
1944
100.00
0.180
2010
97.90
0.262
2097
98.50
0.340
2173
99.90
0.448
2168
97.40
PE4
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
NA
SODIUM ION
HOH
water
Synthetic peptide
sample
PE4
6061
2
PE4
PE4
101
B
NA
1
3
NA
NA
102
B
PE4
6061
2
PE4
PE4
101
C
HOH
8
4
HOH
HOH
101
A
HOH
14
4
HOH
HOH
102
A
HOH
18
4
HOH
HOH
103
A
HOH
22
4
HOH
HOH
104
A
HOH
26
4
HOH
HOH
105
A
HOH
28
4
HOH
HOH
106
A
HOH
30
4
HOH
HOH
107
A
HOH
39
4
HOH
HOH
108
A
HOH
41
4
HOH
HOH
109
A
HOH
50
4
HOH
HOH
110
A
HOH
52
4
HOH
HOH
111
A
HOH
56
4
HOH
HOH
112
A
HOH
3
4
HOH
HOH
201
B
HOH
5
4
HOH
HOH
202
B
HOH
12
4
HOH
HOH
203
B
HOH
17
4
HOH
HOH
204
B
HOH
31
4
HOH
HOH
205
B
HOH
32
4
HOH
HOH
206
B
HOH
33
4
HOH
HOH
207
B
HOH
36
4
HOH
HOH
208
B
HOH
43
4
HOH
HOH
209
B
HOH
45
4
HOH
HOH
210
B
HOH
47
4
HOH
HOH
211
B
HOH
48
4
HOH
HOH
212
B
HOH
51
4
HOH
HOH
213
B
HOH
1
4
HOH
HOH
201
C
HOH
4
4
HOH
HOH
202
C
HOH
7
4
HOH
HOH
203
C
HOH
13
4
HOH
HOH
204
C
HOH
15
4
HOH
HOH
205
C
HOH
16
4
HOH
HOH
206
C
HOH
21
4
HOH
HOH
207
C
HOH
23
4
HOH
HOH
208
C
HOH
24
4
HOH
HOH
209
C
HOH
29
4
HOH
HOH
210
C
HOH
44
4
HOH
HOH
211
C
HOH
46
4
HOH
HOH
212
C
HOH
10
4
HOH
HOH
213
C
HOH
2
4
HOH
HOH
101
D
HOH
6
4
HOH
HOH
102
D
HOH
9
4
HOH
HOH
103
D
HOH
11
4
HOH
HOH
104
D
HOH
20
4
HOH
HOH
105
D
HOH
34
4
HOH
HOH
106
D
HOH
42
4
HOH
HOH
107
D
HOH
49
4
HOH
HOH
108
D
HOH
53
4
HOH
HOH
109
D
HOH
54
4
HOH
HOH
110
D
HOH
55
4
HOH
HOH
111
D
LYS
1
n
1
LYS
1
A
ASP
2
n
2
ASP
2
A
TRP
3
n
3
TRP
3
A
SER
4
n
4
SER
4
A
PHE
5
n
5
PHE
5
A
TYR
6
n
6
TYR
6
A
LYS
1
n
1
LYS
1
B
ASP
2
n
2
ASP
2
B
TRP
3
n
3
TRP
3
B
SER
4
n
4
SER
4
B
PHE
5
n
5
PHE
5
B
TYR
6
n
6
TYR
6
B
LYS
1
n
1
LYS
1
C
ASP
2
n
2
ASP
2
C
TRP
3
n
3
TRP
3
C
SER
4
n
4
SER
4
C
PHE
5
n
5
PHE
5
C
TYR
6
n
6
TYR
6
C
LYS
1
n
1
LYS
1
D
ASP
2
n
2
ASP
2
D
TRP
3
n
3
TRP
3
D
SER
4
n
4
SER
4
D
PHE
5
n
5
PHE
5
D
TYR
6
n
6
TYR
6
D
software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PISA
2
dimeric
890
-9
2030
690
-5
2120
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ASP
2
A
N
ASP
2
B
O
TYR
6
B
O
TYR
6
C
N
SER
4
C
N
SER
4
D
O
SER
4
D
O
SER
4
1
B
O1
PE4
101
E
O1
PE4
1
1
N
1
B
C1
PE4
101
E
C1
PE4
1
1
N
1
B
C2
PE4
101
E
C2
PE4
1
1
N
1
B
O7
PE4
101
E
O7
PE4
1
1
N
1
B
C13
PE4
101
E
C13
PE4
1
1
N
1
B
C14
PE4
101
E
C14
PE4
1
1
N
1
B
O8
PE4
101
E
O8
PE4
1
1
N
1
B
C15
PE4
101
E
C15
PE4
1
1
N
1
B
C16
PE4
101
E
C16
PE4
1
1
N
1
C
O1
PE4
101
G
O1
PE4
1
1
N
1
C
C1
PE4
101
G
C1
PE4
1
1
N
1
C
C2
PE4
101
G
C2
PE4
1
1
N
1
C
O7
PE4
101
G
O7
PE4
1
1
N
1
C
C13
PE4
101
G
C13
PE4
1
1
N
1
C
C14
PE4
101
G
C14
PE4
1
1
N
1
C
O8
PE4
101
G
O8
PE4
1
1
N
1
C
C15
PE4
101
G
C15
PE4
1
1
N
1
C
C16
PE4
101
G
C16
PE4
1
1
N
48.940
10.9748
1.730
0.2207
-0.0000
-0.0000
0.2207
-0.0000
-0.4415
0.1311
0.1119
0.1138
0.9700
14.9810
1601
15997
10.0100
99.8400
1.000
0.130
0.9532
0.0600
1
2.010
SIRAS
9.1500
0.7700
0.9000
ML
FLAT BULK SOLVENT MODEL
38.5410
0.4070
0.9700
14.9810
49
324
31
0
244
0.010
369
1.417
495
0.095
37
0.009
58
19.613
163
0.1713
0.1495
1.0016
140
1251
1391
11
99.0000
0.1571
0.1342
1.0374
144
1303
1447
11
100.0000
0.1138
0.1072
1.0789
145
1301
1446
11
100.0000
0.1088
0.0908
1.1280
142
1278
1420
11
100.0000
0.1048
0.0891
1.1874
144
1299
1443
11
100.0000
0.1198
0.0941
1.2618
144
1291
1435
11
100.0000
0.1238
0.0961
1.3592
146
1316
1462
11
100.0000
0.1029
0.0982
1.4958
146
1314
1460
11
100.0000
0.1325
0.1003
1.7120
147
1320
1467
11
100.0000
0.1349
0.1075
2.1559
147
1330
1477
11
100.0000
0.1445
0.1304
14.9826
156
1393
1549
11
99.0000
9.162
0.970
14.9810
4E0K
-3.000
0.069
1
12.660
99.300
0.448
0.970
1.000
2.420
5383
2168
1
97.400
0.340
1.000
1.020
3.080
5490
2173
1
99.900
0.262
1.020
1.050
3.820
5435
2097
1
98.500
0.180
1.050
1.080
4.890
5364
2010
1
97.900
0.147
1.080
1.120
5.690
5159
1944
1
100.000
0.122
1.120
1.160
6.680
5411
1981
1
99.300
0.110
1.160
1.200
7.220
5033
1795
1
98.500
0.144
1.200
1.250
9.170
9045
1788
1
100.000
0.140
1.250
1.310
11.090
11764
1769
1
100.000
0.120
1.310
1.370
13.160
10607
1583
1
100.000
0.102
1.370
1.450
15.660
10676
1599
1
100.000
0.088
1.450
1.530
18.100
9680
1437
1
100.000
0.080
1.530
1.640
20.790
9283
1400
1
100.000
0.071
1.640
1.770
23.720
8510
1286
1
100.000
0.067
1.770
1.940
26.120
8047
1224
1
100.000
0.062
1.940
2.170
29.010
6712
1039
1
100.000
0.058
2.170
2.510
29.890
6277
949
1
100.000
0.060
2.510
3.070
31.340
5165
806
1
99.800
0.046
3.070
4.340
31.900
3330
599
1
98.200
0.043
4.340
31.180
1568
326
1
95.000
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.7_650
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2 Microglobulin (58-63)
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
2
N
N
4
N
N
4
N
N
4
N
N
4
N
N
metalc
2.831
B
B
ASP
2
B
OD1
ASP
2
1_555
B
NA
102
F
NA
NA
1_555
PROTEIN FIBRIL
amyloid, out-of-register, fiber-forming, PROTEIN FIBRIL
4E0K
PDB
1
4E0K
1
6
4E0K
1
6
4E0K
A
1
1
6
1
6
4E0K
1
6
4E0K
B
1
1
6
1
6
4E0K
1
6
4E0K
C
1
1
6
1
6
4E0K
1
6
4E0K
D
1
1
6
2
2
anti-parallel
anti-parallel
A
ASP
2
A
ASP
2
A
PHE
5
A
PHE
5
B
TRP
3
B
TRP
3
B
TYR
6
B
TYR
6
C
TRP
3
C
TRP
3
C
PHE
5
C
PHE
5
D
TRP
3
D
TRP
3
D
PHE
5
D
PHE
5
BINDING SITE FOR RESIDUE PE4 B 101
B
PE4
101
Software
14
BINDING SITE FOR RESIDUE NA B 102
B
NA
102
Software
5
BINDING SITE FOR RESIDUE PE4 C 101
C
PE4
101
Software
10
A
TRP
3
A
TRP
3
14
6_555
A
TYR
6
A
TYR
6
14
1_556
A
HOH
103
H
HOH
14
6_555
B
TRP
3
B
TRP
3
14
6_555
B
PHE
5
B
PHE
5
14
6_554
B
TYR
6
B
TYR
6
14
1_555
B
HOH
203
I
HOH
14
1_555
B
HOH
207
I
HOH
14
1_555
B
HOH
208
I
HOH
14
1_556
B
HOH
208
I
HOH
14
1_555
C
TRP
3
C
TRP
3
14
1_556
C
TRP
3
C
TRP
3
14
1_555
D
TRP
3
D
TRP
3
14
1_555
D
PHE
5
D
PHE
5
14
1_556
A
PHE
5
A
PHE
5
5
1_556
B
ASP
2
B
ASP
2
5
1_555
B
TRP
3
B
TRP
3
5
1_555
D
LYS
1
D
LYS
1
5
5_554
D
HOH
109
K
HOH
5
5_554
C
TYR
6
C
TYR
6
10
3_544
C
TYR
6
C
TYR
6
10
2_444
C
TYR
6
C
TYR
6
10
2_445
C
HOH
206
J
HOH
10
3_544
C
HOH
206
J
HOH
10
3_543
C
HOH
206
J
HOH
10
1_554
C
HOH
206
J
HOH
10
2_444
D
TYR
6
D
TYR
6
10
3_545
D
TYR
6
D
TYR
6
10
2_445
D
TYR
6
D
TYR
6
10
3_544
169
P 61